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Programming For Biologists

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  • Python Inferno

Lectures - 2010

Introduction

Expressions, types, variables & errors

Functions

Strings - No lecture, just read the book

Modules 1

Introduction to Databases

Introduction to Queries - No slides

Making your own modules

Program structure

Introduction to lists

Lists - slicing, looping and dealing with aliasing

Lists - list methods, nested lists, and importing data into lists

Import comma delimited text example

More information on lists including a complete list (heh heh) of list methods

Databases - Basic Joins

Database Structure & Advance Joins

Databases - Nested Querie

Loops - while loops

Control statements

Programming style & Documenting code

Problem decomposition

Problem decomposition steps

Basic debugging

Debugging with a debugger - no slides

Software Carpentry 3.0 notes on using a debugger

Working with data in files

Exporting data from Base

Importing data into Python

Exporting data from Python

Introduction to Numpy

Introduction to Matplotlib

Introduction to Statistics in Scipy

Adv. Databases - Queries in SQL, Accessing data directly from Python

Intro to Bioinformatics in Python

  • Biopython Data Types & Methods
  • Running Blast from Python
  • Biopython Tutorial - amazing walk through of Biopython

Secondary links

  • Why Python?
  • Why this class?
  • Acknowledgements

Creative Commons License
This work is licensed under a Creative Commons Attribution 3.0 United States License.